Investigation of Binding Properties of Some Oxime Compounds by Molecular Docking Method

Abstract

In this study, the binding properties of some oxime compounds which have high biological activity potential to the active site of selected proteins were investigated by molecular docking method. All oxime ligand molecules studied for this purpose were optimized in Gaussian09 program using B3LYP function by Density Functional Theory (DFT) and 6-311G(d,p) basic set. HOMO, LUMO and HOMO-LUMO energy gaps of all optimized molecules were calculated. The relationship between quantum chemical parameters and inhibition activities for the ligands studied were also investigated. Binding studies of ligand molecules with molecular docking method by selected proteins were performed using optimized geometries of the ligands. The crystal structures of selected proteins from the Protein Data Bank were provided in *.pdb format and their interaction with optimized ligands was investigated using the SwissDock web server. As a result of the molecular docking studies, ligand-protein binding energies were determined by determining the number of hydrogen bond regions that could occur between the ligand-protein.

Keywords

• Oxime
• DFT
• Protein
• Ligand
• Molecular docking

Bazı Oksim Bileşiklerinin Bağlanma Özelliklerinin Moleküler Kenetlenme Yöntemiyle İncelenmesi

Abstract

Bu çalışmada, biyolojik aktivite gösterme potansiyeli yüksek olan bazı oksim bileşiklerinin, seçilmiş bazı proteinlerin aktif bölgesine bağlanma özellikleri moleküler kenetlenme (Doking) yöntemiyle incelenmiştir. Bu amaçla çalışılan tüm oksim ligand molekülleri, Yoğunluk Fonksiyonel Teorisi (DFT) yöntemiyle B3LYP fonksiyoneli ve 6-311G(d,p) temel seti kullanılarak Gaussian09 programında optimize edilmiştir. Optimize edilen tüm moleküllerin HOMO, LUMO ve HOMO-LUMO enerji farkları hesaplanmıştır. Çalışılan ligandlar için belirlenen kuantum kimyasal parametreleri ve inhibisyon aktiviteleri arasındaki ilişki de araştırılmıştır. Ligand moleküllerinin seçilen proteinlerle moleküler kenetlenme yöntemiyle bağlantı çalışmaları, ligandların optimize edilmiş geometrileri kullanılarak gerçekleştirilmiştir. Protein veri bankasından, seçilen proteinlerin kristal yapıları *.pdb formatında temin edilmiş ve bu kristal yapıların optimize ligandlarla etkileşimi SwissDock web sunucusu kullanılarak incelenmiştir. Moleküler kenetlenme çalışmaları sonucu, ligand-protein bağlanma enerjileri, ligand-protein arasında oluşabilecek hidrojen bağ bölgeleri ve sayısı tespit edilerek değerlendirilmiştir.

Keywords

• Oksim
• DFT
• Protein
• Ligand
• Moleküler kenetlenme

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